In my experience with powdercoating, and I am no expert, but I would do all work and any repairs or modifications before powdercoating.
I have chiped powdercoating in the past and you can't just us a shake and shoot to repair it. I have learned to make sure all work is done before I have my parts powdercoated. I have been real careful about re-assembly as well, can chip with wrench or by hitting parts together.
Good luck.
